[{"year":"2025","acknowledgement":"The author warmly thanks Jan Maas for suggesting the project and for his guidance, and Melchior Wirth and Haonan Zhang for useful discussions. The author is also grateful to an anonymous reviewer for carefully reading the manuscript and providing many valuable suggestions. The author gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme\r\n(grant agreement No. 716117) and by the Austrian Science Fund (FWF), Project SFB F65.","OA_place":"repository","corr_author":"1","publisher":"Institute of Mathematical Statistics","language":[{"iso":"eng"}],"month":"02","_id":"20040","date_updated":"2025-11-05T13:50:07Z","citation":{"chicago":"Pedrotti, Francesco. “Contractive Coupling Rates and Curvature Lower Bounds for Markov Chains.” <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2025. <a href=\"https://doi.org/10.1214/24-aap2113\">https://doi.org/10.1214/24-aap2113</a>.","ista":"Pedrotti F. 2025. Contractive coupling rates and curvature lower bounds for Markov chains. The Annals of Applied Probability. 35(1), 196–250.","short":"F. Pedrotti, The Annals of Applied Probability 35 (2025) 196–250.","apa":"Pedrotti, F. (2025). Contractive coupling rates and curvature lower bounds for Markov chains. <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/24-aap2113\">https://doi.org/10.1214/24-aap2113</a>","ieee":"F. Pedrotti, “Contractive coupling rates and curvature lower bounds for Markov chains,” <i>The Annals of Applied Probability</i>, vol. 35, no. 1. Institute of Mathematical Statistics, pp. 196–250, 2025.","mla":"Pedrotti, Francesco. “Contractive Coupling Rates and Curvature Lower Bounds for Markov Chains.” <i>The Annals of Applied Probability</i>, vol. 35, no. 1, Institute of Mathematical Statistics, 2025, pp. 196–250, doi:<a href=\"https://doi.org/10.1214/24-aap2113\">10.1214/24-aap2113</a>.","ama":"Pedrotti F. Contractive coupling rates and curvature lower bounds for Markov chains. <i>The Annals of Applied Probability</i>. 2025;35(1):196-250. doi:<a href=\"https://doi.org/10.1214/24-aap2113\">10.1214/24-aap2113</a>"},"page":"196 - 250","date_published":"2025-02-01T00:00:00Z","type":"journal_article","isi":1,"ec_funded":1,"arxiv":1,"title":"Contractive coupling rates and curvature lower bounds for Markov chains","author":[{"last_name":"Pedrotti","first_name":"Francesco","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","full_name":"Pedrotti, Francesco"}],"article_processing_charge":"No","publication_identifier":{"issn":["1050-5164"]},"quality_controlled":"1","publication":"The Annals of Applied Probability","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2308.00516","open_access":"1"}],"issue":"1","doi":"10.1214/24-aap2113","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JaMa"}],"project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"day":"01","publication_status":"published","status":"public","volume":35,"date_created":"2025-07-21T07:49:15Z","article_type":"original","related_material":{"record":[{"status":"public","id":"17351","relation":"earlier_version"}]},"abstract":[{"lang":"eng","text":"Contractive coupling rates have been recently introduced by Conforti as a tool to establish convex Sobolev inequalities (including modified log-Sobolev and Poincaré inequality) for some classes of Markov chains. In this work, for most of the examples discussed by Conforti, we use contractive coupling rates to prove stronger inequalities, in the form of curvature lower bounds (in entropic and discrete Bakry–Émery sense) and geodesic convexity of some entropic functionals. In addition, we recall and give straightforward generalizations of some notions of coarse Ricci curvature, and we discuss some of their properties and relations with the concepts of couplings and coupling rates: as an application, we show exponential contraction of the p-Wasserstein distance for the heat flow in the aforementioned examples."}],"OA_type":"green","oa_version":"Preprint","intvolume":"        35","scopus_import":"1","external_id":{"isi":["001434322900006"],"arxiv":["2308.00516"]}},{"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2025-07-22T10:04:57Z","success":1,"file_name":"2025_Evolution_Connallon.pdf","date_created":"2025-07-22T10:04:57Z","file_size":8150623,"checksum":"68c4c996d0e8c9ee3d4fb61bca75b31a","file_id":"20068","creator":"dernst"}],"language":[{"iso":"eng"}],"publisher":"Oxford University Press","_id":"20044","citation":{"apa":"Connallon, T., Czuppon, P., Olito, C., Goedert, D., Kokko, H., Nava-Bolaños, A., … Ruzicka, F. (2025). Predicting the prevalence of genetic trade-offs among adaptive substitutions. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpaf061\">https://doi.org/10.1093/evolut/qpaf061</a>","short":"T. Connallon, P. Czuppon, C. Olito, D. Goedert, H. Kokko, A. Nava-Bolaños, S. Nilén, E.I. Svensson, M. Zwoinska, L. Dutoit, F. Ruzicka, Evolution 79 (2025) 1243–1255.","ista":"Connallon T, Czuppon P, Olito C, Goedert D, Kokko H, Nava-Bolaños A, Nilén S, Svensson EI, Zwoinska M, Dutoit L, Ruzicka F. 2025. Predicting the prevalence of genetic trade-offs among adaptive substitutions. Evolution. 79(7), 1243–1255.","mla":"Connallon, Tim, et al. “Predicting the Prevalence of Genetic Trade-Offs among Adaptive Substitutions.” <i>Evolution</i>, vol. 79, no. 7, Oxford University Press, 2025, pp. 1243–55, doi:<a href=\"https://doi.org/10.1093/evolut/qpaf061\">10.1093/evolut/qpaf061</a>.","ama":"Connallon T, Czuppon P, Olito C, et al. Predicting the prevalence of genetic trade-offs among adaptive substitutions. <i>Evolution</i>. 2025;79(7):1243-1255. doi:<a href=\"https://doi.org/10.1093/evolut/qpaf061\">10.1093/evolut/qpaf061</a>","ieee":"T. Connallon <i>et al.</i>, “Predicting the prevalence of genetic trade-offs among adaptive substitutions,” <i>Evolution</i>, vol. 79, no. 7. Oxford University Press, pp. 1243–1255, 2025.","chicago":"Connallon, Tim, Peter Czuppon, Colin Olito, Debora Goedert, Hanna Kokko, Angela Nava-Bolaños, Sofie Nilén, et al. “Predicting the Prevalence of Genetic Trade-Offs among Adaptive Substitutions.” <i>Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/evolut/qpaf061\">https://doi.org/10.1093/evolut/qpaf061</a>."},"date_updated":"2025-09-30T14:06:38Z","page":"1243-1255","month":"07","year":"2025","OA_place":"publisher","acknowledgement":"Support for this research came from the European Society of Evolutionary Biology (ESEB) through a “Special Topics Network” grant. Further financial support came from the European Research Council (ERC-2023-STG916 #101117517, to C.O.), the Swedish Research Council (#2022-03603, to C.O.; #2020‑03123, to E.I.S.), the Research Council of Norway (Norges forskningsråd #302619, to D.G.), the Alexander von Humboldt Foundation and the GenEvo graduate school (to H.K.), the Foundation for Zoological Research and the Birgitta Sintring Foundation (#S2024-0007, to M.K.Z.), a postdoctoral fellowship from the Consejo Nacional de Humanidades, Ciencias y Tecnología (to A.N.B.), and a H2020 Marie Skłodowska-Curie COFUND Action fellowship (#101034413, to F.R.). We wish to express our deepest gratitude to Lotte de Vries for extensive discussion of the project, rederiving some of our results, and providing comments on an earlier version of the manuscript, and to the European Society of Evolutionary Biology (ESEB) for a “Special Topics Network” grant that supported workshops that initiated this collaboration and facilitated many new ideas and friendships. We also thank two anonymous reviewers for their thoughtful comments and suggestions that helped us to substantially improve upon the original version of the article.","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"publication":"Evolution","ddc":["570"],"date_published":"2025-07-01T00:00:00Z","has_accepted_license":"1","type":"journal_article","ec_funded":1,"isi":1,"author":[{"full_name":"Connallon, Tim","last_name":"Connallon","first_name":"Tim"},{"full_name":"Czuppon, Peter","last_name":"Czuppon","first_name":"Peter"},{"last_name":"Olito","first_name":"Colin","full_name":"Olito, Colin"},{"last_name":"Goedert","first_name":"Debora","full_name":"Goedert, Debora"},{"first_name":"Hanna","last_name":"Kokko","full_name":"Kokko, Hanna"},{"first_name":"Angela","last_name":"Nava-Bolaños","full_name":"Nava-Bolaños, Angela"},{"full_name":"Nilén, Sofie","first_name":"Sofie","last_name":"Nilén"},{"full_name":"Svensson, Erik I","last_name":"Svensson","first_name":"Erik I"},{"last_name":"Zwoinska","first_name":"Martyna","full_name":"Zwoinska, Martyna"},{"last_name":"Dutoit","first_name":"Ludovic","full_name":"Dutoit, Ludovic"},{"full_name":"Ruzicka, Filip","last_name":"Ruzicka","first_name":"Filip","id":"347955dd-57b0-11ee-9095-c28bdd368f4b"}],"title":"Predicting the prevalence of genetic trade-offs among adaptive substitutions","department":[{"_id":"BeVi"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1093/evolut/qpaf061","project":[{"call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"day":"01","publication_status":"published","status":"public","oa":1,"file_date_updated":"2025-07-22T10:04:57Z","PlanS_conform":"1","issue":"7","intvolume":"        79","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["001477180800001"]},"article_type":"original","volume":79,"date_created":"2025-07-21T07:57:28Z","abstract":[{"text":"Genetic trade-offs—which occur when variants that are beneficial in some contexts of natural selection are harmful in others—can influence a wide range of evolutionary phenomena, from the maintenance of genetic variation to the evolution of aging and sex differences. An extensive body of evolutionary theory has focused on the consequences of such trade-offs, and recent analyses of Fisher’s geometric model have further quantified the expected proportion of new mutations that exhibit trade-offs. However, the theory remains silent regarding the prevalence of trade-offs among the variants that contribute to adaptation. Here, we extend Fisher’s geometric model to predict the prevalence of trade-offs among the adaptive mutations that become established or fixed in a population. We consider trade-offs between sexes, habitats, fitness components, and temporally fluctuating environments. In all 4 scenarios, trade-off alleles are consistently under-represented among established relative to new beneficial mutations—an effect that arises from the greater susceptibility of trade-off alleles to genetic drift. Adaptation during a population size decline exacerbates this deficit of trade-offs among established mutations, whereas population expansions dampen it. Consequently, threatened populations should primarily adapt using unconditionally beneficial alleles, while invasive populations are more prone to adaptation using variants that exhibit trade-offs.","lang":"eng"}],"OA_type":"hybrid","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/4.0/"},{"external_id":{"arxiv":["2305.06722"]},"OA_type":"green","oa_version":"Preprint","article_type":"original","date_created":"2025-07-21T07:59:16Z","abstract":[{"lang":"eng","text":"We consider the time evolution of the renormalized Nelson model, which describes N bosons linearly coupled to a quantized scalar field, in the mean-field limit of many particles N≫1 with coupling constant proportional to N^−1/2. First, we show that initial states exhibiting Bose–Einstein condensation for the particles and approximating a coherent state for the quantum field retain their structure under the many-body time evolution. Concretely, the dynamics of the reduced densities are approximated by solutions of two coupled PDEs, the Schrödinger–Klein–Gordon equations. Second, we construct a renormalized Bogoliubov evolution that describes the quantum fluctuations around the Schrödinger–Klein–Gordon equations. This evolution is used to extend the approximation of the evolved many-body state to the full norm topology. In summary, we provide a comprehensive analysis of the Nelson model that reveals the role of renormalization in the mean-field Bogoliubov theory."}],"publication_status":"epub_ahead","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"doi":"10.4171/aihpc/154","day":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.06722"}],"oa":1,"publication":"Annales de l'Institut Henri Poincaré C","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"eissn":["1873-1430"],"issn":["0294-1449"]},"arxiv":1,"author":[{"full_name":"Falconi, Marco","first_name":"Marco","last_name":"Falconi"},{"first_name":"Jonas","last_name":"Lampart","full_name":"Lampart, Jonas"},{"full_name":"Leopold, Nikolai","last_name":"Leopold","first_name":"Nikolai"},{"id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes","last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes"}],"title":"Renormalized Bogoliubov theory for the Nelson model","DOAJ_listed":"1","date_published":"2025-05-06T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"publisher":"EMS Press","_id":"20045","citation":{"ama":"Falconi M, Lampart J, Leopold N, Mitrouskas DJ. Renormalized Bogoliubov theory for the Nelson model. <i>Annales de l’Institut Henri Poincaré C</i>. 2025. doi:<a href=\"https://doi.org/10.4171/aihpc/154\">10.4171/aihpc/154</a>","mla":"Falconi, Marco, et al. “Renormalized Bogoliubov Theory for the Nelson Model.” <i>Annales de l’Institut Henri Poincaré C</i>, EMS Press, 2025, doi:<a href=\"https://doi.org/10.4171/aihpc/154\">10.4171/aihpc/154</a>.","ieee":"M. Falconi, J. Lampart, N. Leopold, and D. J. Mitrouskas, “Renormalized Bogoliubov theory for the Nelson model,” <i>Annales de l’Institut Henri Poincaré C</i>. EMS Press, 2025.","short":"M. Falconi, J. Lampart, N. Leopold, D.J. Mitrouskas, Annales de l’Institut Henri Poincaré C (2025).","apa":"Falconi, M., Lampart, J., Leopold, N., &#38; Mitrouskas, D. J. (2025). Renormalized Bogoliubov theory for the Nelson model. <i>Annales de l’Institut Henri Poincaré C</i>. EMS Press. <a href=\"https://doi.org/10.4171/aihpc/154\">https://doi.org/10.4171/aihpc/154</a>","ista":"Falconi M, Lampart J, Leopold N, Mitrouskas DJ. 2025. Renormalized Bogoliubov theory for the Nelson model. Annales de l’Institut Henri Poincaré C.","chicago":"Falconi, Marco, Jonas Lampart, Nikolai Leopold, and David Johannes Mitrouskas. “Renormalized Bogoliubov Theory for the Nelson Model.” <i>Annales de l’Institut Henri Poincaré C</i>. EMS Press, 2025. <a href=\"https://doi.org/10.4171/aihpc/154\">https://doi.org/10.4171/aihpc/154</a>."},"date_updated":"2025-12-30T07:31:09Z","month":"05","OA_place":"repository","year":"2025"},{"article_processing_charge":"Yes","publication_identifier":{"eissn":["1083-6489"]},"quality_controlled":"1","publication":"Electronic Journal of Probability","ddc":["510"],"date_published":"2025-06-27T00:00:00Z","DOAJ_listed":"1","type":"journal_article","has_accepted_license":"1","isi":1,"arxiv":1,"ec_funded":1,"title":"Extreme eigenvalues of Laplacian random matrices with Gaussian entries","author":[{"full_name":"Campbell, Andrew J","id":"582b06a9-1f1c-11ee-b076-82ffce00dde4","first_name":"Andrew J","last_name":"Campbell"},{"full_name":"Luh, Kyle","last_name":"Luh","first_name":"Kyle"},{"full_name":"O’Rourke, Sean","first_name":"Sean","last_name":"O’Rourke"},{"last_name":"Arenas-Velilla","first_name":"Santiago","full_name":"Arenas-Velilla, Santiago"},{"full_name":"Perez-Abreu, Victor","first_name":"Victor","last_name":"Perez-Abreu"}],"file":[{"success":1,"date_updated":"2025-07-23T08:35:53Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"dernst","file_id":"20069","date_created":"2025-07-23T08:35:53Z","file_size":580591,"checksum":"a7a9f2bb7a6295786c16d4c7bd612621","file_name":"2025_ElectronJourProbab_Campbell.pdf"}],"publisher":"Institute of Mathematical Statistics","corr_author":"1","language":[{"iso":"eng"}],"month":"06","page":"1-52","_id":"20046","date_updated":"2025-09-30T14:07:19Z","citation":{"chicago":"Campbell, Andrew J, Kyle Luh, Sean O’Rourke, Santiago Arenas-Velilla, and Victor Perez-Abreu. “Extreme Eigenvalues of Laplacian Random Matrices with Gaussian Entries.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2025. <a href=\"https://doi.org/10.1214/25-ejp1366\">https://doi.org/10.1214/25-ejp1366</a>.","ista":"Campbell AJ, Luh K, O’Rourke S, Arenas-Velilla S, Perez-Abreu V. 2025. Extreme eigenvalues of Laplacian random matrices with Gaussian entries. Electronic Journal of Probability. 30, 1–52.","short":"A.J. Campbell, K. Luh, S. O’Rourke, S. Arenas-Velilla, V. Perez-Abreu, Electronic Journal of Probability 30 (2025) 1–52.","apa":"Campbell, A. J., Luh, K., O’Rourke, S., Arenas-Velilla, S., &#38; Perez-Abreu, V. (2025). Extreme eigenvalues of Laplacian random matrices with Gaussian entries. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/25-ejp1366\">https://doi.org/10.1214/25-ejp1366</a>","ieee":"A. J. Campbell, K. Luh, S. O’Rourke, S. Arenas-Velilla, and V. Perez-Abreu, “Extreme eigenvalues of Laplacian random matrices with Gaussian entries,” <i>Electronic Journal of Probability</i>, vol. 30. Institute of Mathematical Statistics, pp. 1–52, 2025.","ama":"Campbell AJ, Luh K, O’Rourke S, Arenas-Velilla S, Perez-Abreu V. Extreme eigenvalues of Laplacian random matrices with Gaussian entries. <i>Electronic Journal of Probability</i>. 2025;30:1-52. doi:<a href=\"https://doi.org/10.1214/25-ejp1366\">10.1214/25-ejp1366</a>","mla":"Campbell, Andrew J., et al. “Extreme Eigenvalues of Laplacian Random Matrices with Gaussian Entries.” <i>Electronic Journal of Probability</i>, vol. 30, Institute of Mathematical Statistics, 2025, pp. 1–52, doi:<a href=\"https://doi.org/10.1214/25-ejp1366\">10.1214/25-ejp1366</a>."},"year":"2025","OA_place":"publisher","acknowledgement":"The authors thank Santiago Arenas-Velilla and Victor Pérez-Abreu for comments on an earlier draft of this manuscript and for contributing Appendix A. The authors also thank Yan Fyodorov for providing useful references.\r\nA. Campbell was partially supported by the European Research Council Grant No. 101020331. K. Luh was supported in part by the Ralph E. Powe Junior Faculty Enhancement Award and Simons Foundation Grant MP-TSM-00001988. S. O’Rourke has been supported in part by NSF CAREER grant DMS-2143142. ","intvolume":"        30","external_id":{"arxiv":["2211.17175"],"isi":["001540927000024"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2025-07-21T08:06:18Z","volume":30,"article_type":"original","abstract":[{"text":"A Laplacian matrix is a real symmetric matrix whose row and column sums are zero. We investigate the limiting distribution of the largest eigenvalues of a Laplacian random matrix with Gaussian entries. Unlike many classical matrix ensembles, this random matrix model contains dependent entries. Our main results show that the extreme eigenvalues of this model exhibit Poisson statistics. In particular, after properly shifting and scaling, we show that the largest eigenvalue converges to the Gumbel distribution as the dimension of the matrix tends to infinity. While the largest diagonal entry is also shown to have Gumbel fluctuations, there is a rather surprising difference between its deterministic centering term and the centering term required for the largest eigenvalues.","lang":"eng"}],"OA_type":"gold","oa_version":"Published Version","doi":"10.1214/25-ejp1366","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"LaEr"}],"project":[{"call_identifier":"H2020","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"day":"27","publication_status":"published","status":"public","file_date_updated":"2025-07-23T08:35:53Z","oa":1},{"day":"27","department":[{"_id":"CaHe"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1242/dev.204261","status":"public","publication_status":"published","oa":1,"file_date_updated":"2025-07-23T08:43:01Z","issue":"12","PlanS_conform":"1","intvolume":"       152","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"pmid":["40576478"],"isi":["001525252300001"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"During embryonic development, cell behaviors need to be tightly regulated in time and space. Yet how the temporal and spatial regulations of cell behaviors are interconnected during embryonic development remains elusive. To address this, we turned to zebrafish gastrulation, the process whereby dynamic cell behaviors generate the three principal germ layers of the early embryo. Here, we show that Hoxb cluster genes are expressed in a temporally collinear manner at the blastoderm margin, where mesodermal and endodermal (mesendoderm) progenitor cells are specified and ingress to form mesendoderm/hypoblast. Functional analysis shows that these Hoxb genes regulate the timing of cell ingression: under- or overexpression of Hoxb genes perturb the timing of mesendoderm cell ingression and, consequently, the positioning of these cells along the forming anterior-posterior body axis after gastrulation. Finally, we found that Hoxb genes control the timing of mesendoderm ingression by regulating cellular bleb formation and cell surface fluctuations in the ingressing cells. Collectively, our findings suggest that Hoxb genes interconnect the temporal and spatial pattern of cell behaviors during zebrafish gastrulation by controlling cell surface fluctuations."}],"article_number":"dev204261","article_type":"original","volume":152,"date_created":"2025-07-21T08:10:32Z","oa_version":"Published Version","pmid":1,"OA_type":"hybrid","file":[{"date_created":"2025-07-23T08:43:01Z","checksum":"808d8aa28df79d23fb661838d1fdc1be","file_size":25935563,"file_name":"2025_Development_Moriyama.pdf","creator":"dernst","file_id":"20070","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2025-07-23T08:43:01Z"}],"date_updated":"2025-09-30T14:07:51Z","_id":"20048","citation":{"ieee":"Y. Moriyama, T. Mitsui, and C.-P. J. Heisenberg, “Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation,” <i>Development</i>, vol. 152, no. 12. The Company of Biologists, 2025.","ama":"Moriyama Y, Mitsui T, Heisenberg C-PJ. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. <i>Development</i>. 2025;152(12). doi:<a href=\"https://doi.org/10.1242/dev.204261\">10.1242/dev.204261</a>","mla":"Moriyama, Yuuta, et al. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” <i>Development</i>, vol. 152, no. 12, dev204261, The Company of Biologists, 2025, doi:<a href=\"https://doi.org/10.1242/dev.204261\">10.1242/dev.204261</a>.","ista":"Moriyama Y, Mitsui T, Heisenberg C-PJ. 2025. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. 152(12), dev204261.","apa":"Moriyama, Y., Mitsui, T., &#38; Heisenberg, C.-P. J. (2025). Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.204261\">https://doi.org/10.1242/dev.204261</a>","short":"Y. Moriyama, T. Mitsui, C.-P.J. Heisenberg, Development 152 (2025).","chicago":"Moriyama, Yuuta, Toshiyuki Mitsui, and Carl-Philipp J Heisenberg. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” <i>Development</i>. The Company of Biologists, 2025. <a href=\"https://doi.org/10.1242/dev.204261\">https://doi.org/10.1242/dev.204261</a>."},"month":"06","language":[{"iso":"eng"}],"corr_author":"1","publisher":"The Company of Biologists","year":"2025","acknowledgement":"We thank all the Heisenberg lab members for discussions and comments on the manuscript, and the Bioimaging and Life Science facilities of ISTA for support with microscopy and fish maintenance, respectively. This study was funded by a Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowship and a Japan Science and Technology Agency PRESTO grant (JPMJPR214B) to Y.M. Open Access funding provided by the Japan Science and Technology Agency. Deposited in PMC for immediate release.","OA_place":"publisher","quality_controlled":"1","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"article_processing_charge":"Yes (via OA deal)","ddc":["570"],"publication":"Development","has_accepted_license":"1","type":"journal_article","date_published":"2025-06-27T00:00:00Z","author":[{"last_name":"Moriyama","id":"addc9b8c-67a0-11f0-b374-a2e094825470","first_name":"Yuuta","full_name":"Moriyama, Yuuta","orcid":"0000-0002-2853-8051"},{"first_name":"Toshiyuki","last_name":"Mitsui","full_name":"Mitsui, Toshiyuki"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"title":"Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation","isi":1},{"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2402.04151","open_access":"1"}],"issue":"3","department":[{"_id":"JaMa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1214/25-aap2162","project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"name":"The impact of deleterious mutations on small populations","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8","grant_number":"26293"}],"day":"01","publication_status":"published","status":"public","article_type":"original","date_created":"2025-07-21T08:13:54Z","volume":35,"abstract":[{"text":"We prove upper bounds on the L∞-Wasserstein distance from optimal transport between strongly log-concave probability densities and log-Lipschitz perturbations. In the simplest setting, such a bound amounts to a transport-information inequality involving the L∞-Wasserstein metric and the relative L∞-Fisher information. We show that this inequality can be sharpened significantly in situations where the involved densities are anisotropic. Our proof is based on probabilistic techniques using Langevin dynamics. As an application of these results, we obtain sharp exponential rates of convergence in Fisher’s infinitesimal model from quantitative genetics, generalising recent results by Calvez, Poyato, and Santambrogio in dimension 1 to arbitrary dimensions.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"17352","relation":"earlier_version"}]},"OA_type":"green","oa_version":"Preprint","intvolume":"        35","scopus_import":"1","external_id":{"isi":["001523520000012"],"arxiv":["2402.04151"]},"year":"2025","acknowledgement":"This research was funded in part by the Austrian Science Fund (FWF) project 10.55776/F65 and the Austrian Academy of Science, DOC fellowship nr. 26293.","OA_place":"repository","language":[{"iso":"eng"}],"corr_author":"1","publisher":"Institute of Mathematical Statistics","_id":"20050","page":"1913-1940","date_updated":"2025-09-30T14:12:48Z","citation":{"chicago":"Khudiakova, Kseniia, Jan Maas, and Francesco Pedrotti. “L∞-Optimal Transport of Anisotropic Log-Concave Measures and Exponential Convergence in Fisher’s Infinitesimal Model.” <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2025. <a href=\"https://doi.org/10.1214/25-aap2162\">https://doi.org/10.1214/25-aap2162</a>.","ieee":"K. Khudiakova, J. Maas, and F. Pedrotti, “L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model,” <i>The Annals of Applied Probability</i>, vol. 35, no. 3. Institute of Mathematical Statistics, pp. 1913–1940, 2025.","ama":"Khudiakova K, Maas J, Pedrotti F. L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model. <i>The Annals of Applied Probability</i>. 2025;35(3):1913-1940. doi:<a href=\"https://doi.org/10.1214/25-aap2162\">10.1214/25-aap2162</a>","mla":"Khudiakova, Kseniia, et al. “L∞-Optimal Transport of Anisotropic Log-Concave Measures and Exponential Convergence in Fisher’s Infinitesimal Model.” <i>The Annals of Applied Probability</i>, vol. 35, no. 3, Institute of Mathematical Statistics, 2025, pp. 1913–40, doi:<a href=\"https://doi.org/10.1214/25-aap2162\">10.1214/25-aap2162</a>.","ista":"Khudiakova K, Maas J, Pedrotti F. 2025. L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model. The Annals of Applied Probability. 35(3), 1913–1940.","apa":"Khudiakova, K., Maas, J., &#38; Pedrotti, F. (2025). L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model. <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/25-aap2162\">https://doi.org/10.1214/25-aap2162</a>","short":"K. Khudiakova, J. Maas, F. Pedrotti, The Annals of Applied Probability 35 (2025) 1913–1940."},"month":"06","date_published":"2025-06-01T00:00:00Z","type":"journal_article","arxiv":1,"isi":1,"author":[{"orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia","last_name":"Khudiakova","first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338"},{"first_name":"Francesco","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","last_name":"Pedrotti","full_name":"Pedrotti, Francesco"}],"title":"L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["1050-5164"]},"publication":"The Annals of Applied Probability"},{"conference":{"name":"PODC: Symposium on Principles of Distributed Computing","end_date":"2025-06-20","start_date":"2025-06-16","location":"Huatulco, Mexico"},"year":"2025","OA_place":"publisher","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct, No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/I5862,grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with\r\nadditional funding from the netidee SCIENCE Stiftung, 2020–2024\r\nand the German Research Foundation (DFG), grant 470029389\r\n(FlexNets).","file":[{"checksum":"52976d226f3f691aa519d71c1c718fa5","file_size":2200347,"date_created":"2025-08-04T09:10:55Z","file_name":"2025_PODC_ElHayek.pdf","creator":"dernst","file_id":"20115","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2025-08-04T09:10:55Z"}],"month":"06","_id":"20051","date_updated":"2025-10-16T13:08:45Z","citation":{"short":"A. El-Hayek, R. Elsässer, S. Schmid, in:, Proceedings of the ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2025.","apa":"El-Hayek, A., Elsässer, R., &#38; Schmid, S. (2025). An almost tight lower bound for plurality consensus with undecided state dynamics in the population protocol model. In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>. Huatulco, Mexico: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3732772.3733505\">https://doi.org/10.1145/3732772.3733505</a>","ista":"El-Hayek A, Elsässer R, Schmid S. 2025. An almost tight lower bound for plurality consensus with undecided state dynamics in the population protocol model. Proceedings of the ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing.","mla":"El-Hayek, Antoine, et al. “An Almost Tight Lower Bound for Plurality Consensus with Undecided State Dynamics in the Population Protocol Model.” <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2025, doi:<a href=\"https://doi.org/10.1145/3732772.3733505\">10.1145/3732772.3733505</a>.","ama":"El-Hayek A, Elsässer R, Schmid S. An almost tight lower bound for plurality consensus with undecided state dynamics in the population protocol model. In: <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2025. doi:<a href=\"https://doi.org/10.1145/3732772.3733505\">10.1145/3732772.3733505</a>","ieee":"A. El-Hayek, R. Elsässer, and S. Schmid, “An almost tight lower bound for plurality consensus with undecided state dynamics in the population protocol model,” in <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Huatulco, Mexico, 2025.","chicago":"El-Hayek, Antoine, Robert Elsässer, and Stefan Schmid. “An Almost Tight Lower Bound for Plurality Consensus with Undecided State Dynamics in the Population Protocol Model.” In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery, 2025. <a href=\"https://doi.org/10.1145/3732772.3733505\">https://doi.org/10.1145/3732772.3733505</a>."},"publisher":"Association for Computing Machinery","corr_author":"1","language":[{"iso":"eng"}],"type":"conference","has_accepted_license":"1","date_published":"2025-06-13T00:00:00Z","title":"An almost tight lower bound for plurality consensus with undecided state dynamics in the population protocol model","author":[{"orcid":"0000-0003-4268-7368","first_name":"Antoine","id":"888a098e-fcac-11ee-aff7-d347be57b725","last_name":"El-Hayek","full_name":"El-Hayek, Antoine"},{"last_name":"Elsässer","first_name":"Robert","full_name":"Elsässer, Robert"},{"full_name":"Schmid, Stefan","first_name":"Stefan","last_name":"Schmid"}],"isi":1,"arxiv":1,"ec_funded":1,"publication_identifier":{"isbn":[" 9798400718854"]},"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","ddc":["000"],"publication":"Proceedings of the ACM Symposium on Principles of Distributed Computing","file_date_updated":"2025-08-04T09:10:55Z","oa":1,"project":[{"name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","call_identifier":"H2020"},{"grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"day":"13","doi":"10.1145/3732772.3733505","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MoHe"}],"status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"We revisit the majority problem in the population protocol communication model, as first studied by Angluin et al. (Distributed Computing 2008). We consider a more general version of this problem known as plurality consensus, which has already been studied intensively in the literature. In this problem, each node in a system of n nodes, has initially one of k different opinions, and they need to agree on the (relative) majority opinion. In particular, we consider the important and intensively studied model of Undecided State Dynamics.\r\nOur main contribution is an almost tight lower bound on the stabilization time: we prove that there exists an initial configuration, even with bias \\Delta = \\omega(\\sqrt{n\\log n}), where stabilization requires \\Omega(kn\\log \\frac {\\sqrt n} {k \\log n}) interactions, or equivalently, \\Omega(k\\log \\frac {\\sqrt n} {k \\log n}) parallel time for any k = o\\left(\\frac {\\sqrt n}{\\log n}\\right). This bound is tight for any k \\le n^{\\frac 1 2 - \\epsilon}, where \\epsilon >0 can be any small constant, as Amir et al.~(PODC'23) gave a O(k\\log n) parallel time upper bound for k = O\\left(\\frac {\\sqrt n} {\\log ^2 n}\\right)."}],"date_created":"2025-07-21T08:16:15Z","oa_version":"Published Version","OA_type":"hybrid","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"arxiv":["2505.02765"],"isi":["001525534800066"]}},{"ddc":["000"],"publication":"Proceedings of the ACM Symposium on Principles of Distributed Computing","publication_identifier":{"isbn":["9798400718854"]},"quality_controlled":"1","article_processing_charge":"No","title":"Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols","author":[{"last_name":"Breitkopf","first_name":"Tom-Lukas","full_name":"Breitkopf, Tom-Lukas"},{"last_name":"Dallot","first_name":"Julien","full_name":"Dallot, Julien"},{"orcid":"0000-0003-4268-7368","id":"888a098e-fcac-11ee-aff7-d347be57b725","first_name":"Antoine","last_name":"El-Hayek","full_name":"El-Hayek, Antoine"},{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"}],"isi":1,"ec_funded":1,"type":"conference","has_accepted_license":"1","date_published":"2025-06-13T00:00:00Z","month":"06","citation":{"ieee":"T.-L. Breitkopf, J. Dallot, A. El-Hayek, and S. Schmid, “Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols,” in <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Huatulco, Mexico, 2025, pp. 549–552.","ama":"Breitkopf T-L, Dallot J, El-Hayek A, Schmid S. Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols. In: <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2025:549-552. doi:<a href=\"https://doi.org/10.1145/3732772.3733512\">10.1145/3732772.3733512</a>","mla":"Breitkopf, Tom-Lukas, et al. “Brief Announcement: Minimizing Energy Solves Relative Majority with a Cubic Number of States in Population Protocols.” <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2025, pp. 549–52, doi:<a href=\"https://doi.org/10.1145/3732772.3733512\">10.1145/3732772.3733512</a>.","ista":"Breitkopf T-L, Dallot J, El-Hayek A, Schmid S. 2025. Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols. Proceedings of the ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 549–552.","apa":"Breitkopf, T.-L., Dallot, J., El-Hayek, A., &#38; Schmid, S. (2025). Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols. In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i> (pp. 549–552). Huatulco, Mexico: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3732772.3733512\">https://doi.org/10.1145/3732772.3733512</a>","short":"T.-L. Breitkopf, J. Dallot, A. El-Hayek, S. Schmid, in:, Proceedings of the ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2025, pp. 549–552.","chicago":"Breitkopf, Tom-Lukas, Julien Dallot, Antoine El-Hayek, and Stefan Schmid. “Brief Announcement: Minimizing Energy Solves Relative Majority with a Cubic Number of States in Population Protocols.” In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, 549–52. Association for Computing Machinery, 2025. <a href=\"https://doi.org/10.1145/3732772.3733512\">https://doi.org/10.1145/3732772.3733512</a>."},"_id":"20052","date_updated":"2026-02-16T11:46:37Z","page":"549-552","corr_author":"1","publisher":"Association for Computing Machinery","language":[{"iso":"eng"}],"file":[{"file_size":549706,"checksum":"e99679ffb28877b7cea4d54860302790","date_created":"2025-08-05T07:32:01Z","file_name":"2025_PODC_Breitkopf.pdf","creator":"dernst","file_id":"20123","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2025-08-05T07:32:01Z"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct, No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung, 2020–2024 and the German Research Foundation (DFG), grant 470029389 (FlexNets). ","OA_place":"publisher","conference":{"name":"PODC: Symposium on Principles of Distributed Computing","location":"Huatulco, Mexico","start_date":"2025-06-16","end_date":"2025-06-20"},"year":"2025","external_id":{"isi":["001525534800069"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","OA_type":"hybrid","abstract":[{"lang":"eng","text":"This paper revisits a fundamental distributed computing problem in the population protocol model. Provided n agents each starting with an input color in [k], the relative majority problem asks to find the predominant color. In the population protocol model, at each time step, a scheduler selects two agents that first learn each other's states and then update their states based on what they learned.\r\nWe present the Circles protocol that solves the relative majority problem with k3 states. It is always-correct under weakly fair scheduling. Not only does it improve upon the best known upper bound of O(k7), but it also shows a strikingly simpler design inspired by energy minimization in chemical settings."}],"date_created":"2025-07-21T08:17:04Z","status":"public","publication_status":"published","day":"13","project":[{"name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020"},{"grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"doi":"10.1145/3732772.3733512","department":[{"_id":"MoHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-08-05T07:32:01Z","oa":1},{"status":"public","publication_status":"published","day":"13","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020"}],"department":[{"_id":"KrCh"},{"_id":"KrPi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/3732772.3733544","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2025/745"}],"file_date_updated":"2025-08-05T07:15:31Z","oa":1,"external_id":{"isi":["001525534800030"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","OA_type":"hybrid","abstract":[{"lang":"eng","text":"Liquid democracy is a transitive vote delegation mechanism over voting graphs. It enables each voter to delegate their vote(s) to another better-informed voter, with the goal of collectively making a better decision. The question of whether liquid democracy outperforms direct voting has been previously studied in the context of local delegation mechanisms (where voters can only delegate to someone in their neighbourhood) and binary decision problems. It has previously been shown that it is impossible for local delegation mechanisms to outperform direct voting in general graphs. This raises the question: for which classes of graphs do local delegation mechanisms yield good results?\r\nIn this work, we analyse (1) properties of specific graphs and (2) properties of local delegation mechanisms on these graphs, determining where local delegation actually outperforms direct voting. We show that a critical graph property enabling liquid democracy is that the voting outcome of local delegation mechanisms preserves a sufficient amount of variance, thereby avoiding situations where delegation falls behind direct voting1. These insights allow us to prove our main results, namely that there exist local delegation mechanisms that perform no worse and in fact quantitatively better than direct voting in natural graph topologies like complete, random d-regular, and bounded degree graphs, lending a more nuanced perspective to previous impossibility results."}],"date_created":"2025-07-21T08:18:26Z","_id":"20053","date_updated":"2026-02-16T11:46:51Z","citation":{"chicago":"Chatterjee, Krishnendu, Seth Gilbert, Stefan Schmid, Jakub Svoboda, and Michelle X Yeo. “When Is Liquid Democracy Possible?: On the Manipulation of Variance.” In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, 241–51. Association for Computing Machinery, 2025. <a href=\"https://doi.org/10.1145/3732772.3733544\">https://doi.org/10.1145/3732772.3733544</a>.","ieee":"K. Chatterjee, S. Gilbert, S. Schmid, J. Svoboda, and M. X. Yeo, “When is liquid democracy possible?: On the manipulation of variance,” in <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Huatulco, Mexico, 2025, pp. 241–251.","mla":"Chatterjee, Krishnendu, et al. “When Is Liquid Democracy Possible?: On the Manipulation of Variance.” <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2025, pp. 241–51, doi:<a href=\"https://doi.org/10.1145/3732772.3733544\">10.1145/3732772.3733544</a>.","ama":"Chatterjee K, Gilbert S, Schmid S, Svoboda J, Yeo MX. When is liquid democracy possible?: On the manipulation of variance. In: <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2025:241-251. doi:<a href=\"https://doi.org/10.1145/3732772.3733544\">10.1145/3732772.3733544</a>","ista":"Chatterjee K, Gilbert S, Schmid S, Svoboda J, Yeo MX. 2025. When is liquid democracy possible?: On the manipulation of variance. Proceedings of the ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 241–251.","apa":"Chatterjee, K., Gilbert, S., Schmid, S., Svoboda, J., &#38; Yeo, M. X. (2025). When is liquid democracy possible?: On the manipulation of variance. In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i> (pp. 241–251). Huatulco, Mexico: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3732772.3733544\">https://doi.org/10.1145/3732772.3733544</a>","short":"K. Chatterjee, S. Gilbert, S. Schmid, J. Svoboda, M.X. Yeo, in:, Proceedings of the ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2025, pp. 241–251."},"page":"241-251","month":"06","language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","corr_author":"1","file":[{"date_updated":"2025-08-05T07:15:31Z","access_level":"open_access","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"20122","creator":"dernst","file_name":"2025_PODC_Chatterjee.pdf","checksum":"cd628fe54d96e9fc6cc789bb8145422b","file_size":783297,"date_created":"2025-08-05T07:15:31Z"}],"OA_place":"publisher","acknowledgement":"This work was partially supported by MOE-T2EP20122-0014 (DataDriven Distributed Algorithms), German Research Foundation (DFG) project ReNO (SPP 2378) from 2023-2027, ERC CoG 863818 (ForMSMArt) and Austrian Science Fund (FWF) 10.55776/COE12.","year":"2025","conference":{"end_date":"2025-06-20","location":"Huatulco, Mexico","start_date":"2025-06-16","name":"PODC: Symposium on Principles of Distributed Computing"},"ddc":["000"],"publication":"Proceedings of the ACM Symposium on Principles of Distributed Computing","quality_controlled":"1","publication_identifier":{"isbn":["9798400718854"]},"article_processing_charge":"No","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Gilbert","first_name":"Seth","full_name":"Gilbert, Seth"},{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"},{"first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267"},{"full_name":"Yeo, Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X","orcid":"0009-0001-3676-4809"}],"title":"When is liquid democracy possible?: On the manipulation of variance","ec_funded":1,"isi":1,"type":"conference","has_accepted_license":"1","date_published":"2025-06-13T00:00:00Z"},{"oa_version":"None","author":[{"full_name":"Horta, Sharona","first_name":"Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","last_name":"Horta"}],"title":"Solid state diffusion in metal-semiconductors core-shell nanoparticle","type":"conference_abstract","article_number":"220","date_published":"2025-03-03T00:00:00Z","date_created":"2025-07-21T08:22:29Z","publication":"Proceedings of the MATSUS Spring 2025 Conference","quality_controlled":"1","article_processing_charge":"No","year":"2025","conference":{"location":"Sevilla, Spain","start_date":"2025-03-03","end_date":"2025-03-07","name":"MATSUS: Materials for Sustainable Development Conference"},"date_updated":"2025-09-23T09:04:03Z","_id":"20054","status":"public","citation":{"chicago":"Horta, Sharona. “Solid State Diffusion in Metal-Semiconductors Core-Shell Nanoparticle.” In <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Fundació de la comunitat valenciana SCITO, 2025. <a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.220\">https://doi.org/10.29363/nanoge.matsusspring.2025.220</a>.","short":"S. Horta, in:, Proceedings of the MATSUS Spring 2025 Conference, Fundació de la comunitat valenciana SCITO, 2025.","apa":"Horta, S. (2025). Solid state diffusion in metal-semiconductors core-shell nanoparticle. In <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Sevilla, Spain: Fundació de la comunitat valenciana SCITO. <a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.220\">https://doi.org/10.29363/nanoge.matsusspring.2025.220</a>","ista":"Horta S. 2025. Solid state diffusion in metal-semiconductors core-shell nanoparticle. Proceedings of the MATSUS Spring 2025 Conference. MATSUS: Materials for Sustainable Development Conference, 220.","mla":"Horta, Sharona. “Solid State Diffusion in Metal-Semiconductors Core-Shell Nanoparticle.” <i>Proceedings of the MATSUS Spring 2025 Conference</i>, 220, Fundació de la comunitat valenciana SCITO, 2025, doi:<a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.220\">10.29363/nanoge.matsusspring.2025.220</a>.","ama":"Horta S. Solid state diffusion in metal-semiconductors core-shell nanoparticle. In: <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Fundació de la comunitat valenciana SCITO; 2025. doi:<a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.220\">10.29363/nanoge.matsusspring.2025.220</a>","ieee":"S. Horta, “Solid state diffusion in metal-semiconductors core-shell nanoparticle,” in <i>Proceedings of the MATSUS Spring 2025 Conference</i>, Sevilla, Spain, 2025."},"month":"03","publication_status":"published","language":[{"iso":"eng"}],"publisher":"Fundació de la comunitat valenciana SCITO","corr_author":"1","day":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaIb"}],"doi":"10.29363/nanoge.matsusspring.2025.220"},{"OA_type":"closed access","title":"Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case","author":[{"orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee"},{"orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","last_name":"Balazs","first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"last_name":"Horta","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","first_name":"Sharona","full_name":"Horta, Sharona"},{"last_name":"Rayaroth Puthiyaveettil","first_name":"Aiswarya","id":"8aceb01b-8972-11ed-ae7b-d5fe53775add","full_name":"Rayaroth Puthiyaveettil, Aiswarya"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"}],"oa_version":"None","date_published":"2025-03-15T00:00:00Z","date_created":"2025-07-21T08:33:20Z","type":"conference","article_number":"173","abstract":[{"text":"Supercrystals represent three-dimensional orderings of colloidal nanocrystals (NCs), showcasing collective properties in photonics, phononics, and electronics applications.1,2 Recent studies have shown that such assemblies are directly produced during nanocrystal reactions.3–6 However, a fundamental understanding of in situ formed supercrystals that withstand typical NC purification processes remains underexplored, which is important for further use. Herein, we report the reaction precursor-mediated formation of stable PbTe supercrystals. Rationalizing the formation of these assemblies through small-angle x-ray scattering (SAXS) measurements, we unveil their formation mechanism. Our findings reveal that the supercrystal formation occurs in the presence of an excess of lead oleates in the crude solution. It should be noted that the formed supercrystals can be stabilized under specific conditions determined by the lead oleate cluster concentration, content of trioctylphosphine telluride (TOP-Te), NC size and the need of an annealing step at mild conditions. Furthermore, this approach allows for the continuous growth of a secondary phase within the supercrystal; for example in the case of PbTe supercrystals, a PbS shell can be grown on each PbTe NC constituent, resulting in core-shell PbTe-PbS supercrystals. Our work elucidates that reaction precursors play an important role in in situ SC formation and stabilization, implying the possibility of applying this knowledge to other NC reactions.","lang":"eng"}],"publication":"Proceedings of the MATSUS Spring 2025 Conference","article_processing_charge":"No","quality_controlled":"1","acknowledgement":"ISTA and the Werner Siemens Foundation financially supported this work. The Scientific Service Units (SSU) of ISTA supported this research through resources provided by the Electron Microscopy Facility (EMF), NMR Facility and the Lab Support Facility (LSF).","conference":{"end_date":"2025-03-07","start_date":"2025-03-03","location":"Sevilla, Spain","name":"MATSUS: Materials for Sustainable Development Conference"},"year":"2025","publisher":"Fundació de la comunitat valenciana SCITO","corr_author":"1","language":[{"iso":"eng"}],"publication_status":"published","month":"03","_id":"20055","status":"public","citation":{"ieee":"S. Lee, D. Balazs, S. Horta, A. Rayaroth Puthiyaveettil, and M. Ibáñez, “Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case,” in <i>Proceedings of the MATSUS Spring 2025 Conference</i>, Sevilla, Spain, 2025.","mla":"Lee, Seungho, et al. “Reaction Precursor-Mediated Formation of Stable Supercrystals in Colloidal Nanocrystal Synthesis: PbTe Case.” <i>Proceedings of the MATSUS Spring 2025 Conference</i>, 173, Fundació de la comunitat valenciana SCITO, 2025, doi:<a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">10.29363/nanoge.matsusspring.2025.173</a>.","ama":"Lee S, Balazs D, Horta S, Rayaroth Puthiyaveettil A, Ibáñez M. Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case. In: <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Fundació de la comunitat valenciana SCITO; 2025. doi:<a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">10.29363/nanoge.matsusspring.2025.173</a>","ista":"Lee S, Balazs D, Horta S, Rayaroth Puthiyaveettil A, Ibáñez M. 2025. Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case. Proceedings of the MATSUS Spring 2025 Conference. MATSUS: Materials for Sustainable Development Conference, 173.","apa":"Lee, S., Balazs, D., Horta, S., Rayaroth Puthiyaveettil, A., &#38; Ibáñez, M. (2025). Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case. In <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Sevilla, Spain: Fundació de la comunitat valenciana SCITO. <a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">https://doi.org/10.29363/nanoge.matsusspring.2025.173</a>","short":"S. Lee, D. Balazs, S. Horta, A. Rayaroth Puthiyaveettil, M. Ibáñez, in:, Proceedings of the MATSUS Spring 2025 Conference, Fundació de la comunitat valenciana SCITO, 2025.","chicago":"Lee, Seungho, Daniel Balazs, Sharona Horta, Aiswarya Rayaroth Puthiyaveettil, and Maria Ibáñez. “Reaction Precursor-Mediated Formation of Stable Supercrystals in Colloidal Nanocrystal Synthesis: PbTe Case.” In <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Fundació de la comunitat valenciana SCITO, 2025. <a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">https://doi.org/10.29363/nanoge.matsusspring.2025.173</a>."},"date_updated":"2026-02-19T09:25:57Z","doi":"10.29363/nanoge.matsusspring.2025.173","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NMR"},{"_id":"LifeSc"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"day":"15","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}]},{"issue":"4","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2205.02645","open_access":"1"}],"publication_status":"published","status":"public","doi":"10.1086/734083","department":[{"_id":"EdHa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"day":"01","OA_type":"green","pmid":1,"oa_version":"Preprint","volume":205,"date_created":"2025-07-21T08:37:27Z","article_type":"original","related_material":{"record":[{"id":"20121","relation":"software","status":"public"}]},"abstract":[{"text":"Theoretical studies have shown that stochasticity can affect the dynamics of ecosystems in counterintuitive ways. However, without knowing the equations governing the dynamics of populations or ecosystems, it is difficult to ascertain the role of stochasticity in real datasets. Therefore, the inverse problem of inferring the governing stochastic equations from datasets is important. Here, we present an equation discovery methodology that takes time series data of state variables as input and outputs a stochastic differential equation. We achieve this by combining traditional approaches from stochastic calculus with the equation discovery techniques. We demonstrate the generality of the method via several applications. First, we deliberately choose various stochastic models with fundamentally different governing equations, yet they produce nearly identical steady-state distributions. We show that we can recover the correct underlying equations, and thus infer the structure of their stability, accurately from the analysis of time series data alone. We demonstrate our method on two real-world datasets—fish schooling and single-cell migration—that have vastly different spatiotemporal scales and dynamics. We illustrate various limitations and potential pitfalls of the method and how to overcome them via diagnostic measures. Finally, we provide our open-source code via a package named PyDaDDy (Python Library for Data-Driven Dynamics).","lang":"eng"}],"external_id":{"arxiv":["2205.02645"],"isi":["001433250500001"],"pmid":["40179429"]},"intvolume":"       205","acknowledgement":"V.G. acknowledges support from the Science and Engi-neering Research Board, Department of Biotechnology,and the Indo-French Centre for the Promotion of Ad-vanced Research (64T4-1). D.R.M. acknowledges supportfrom a Department of Science and Technology (DST) In-novation in Science Pursuit for Inspired Research (IN-SPIRE) Faculty Award. J.J. acknowledges support froma Humboldt postdoctoral fellowship and the Heidelber-ger Akademie der Wissenschaften, Heidelberg, Germany.D.B.B. acknowledges support from the NOMIS Founda-tion and an European Molecular Biology Organization(EMBO) postdoctoral fellowship (ALTF 343-2022). A.N.and S.P. acknowledge support from Ministry of Educa-tion (MoE) PhD fellowships. We thank Ashrit Mangal-wedhekar, Vivek Jadhav, Shikhara Bhat, Cassandre Aimon,and Harishankar Muppirala for comments on the manu-script and code. We thank Kollegala Sharma for his inputon the Kannada translation of the title and abstract.Data-Driven Model Discovery E115","OA_place":"repository","year":"2025","publisher":"University of Chicago Press","language":[{"iso":"eng"}],"month":"04","citation":{"chicago":"Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar, David Brückner, Danny Raj M, and Vishwesha Guttal. “Discovering Stochastic Dynamical Equations from Ecological Time Series Data.” <i>The American Naturalist</i>. University of Chicago Press, 2025. <a href=\"https://doi.org/10.1086/734083\">https://doi.org/10.1086/734083</a>.","ama":"Nabeel A, Karichannavar A, Palathingal S, et al. Discovering stochastic dynamical equations from ecological time series data. <i>The American Naturalist</i>. 2025;205(4):E100-E117. doi:<a href=\"https://doi.org/10.1086/734083\">10.1086/734083</a>","mla":"Nabeel, Arshed, et al. “Discovering Stochastic Dynamical Equations from Ecological Time Series Data.” <i>The American Naturalist</i>, vol. 205, no. 4, University of Chicago Press, 2025, pp. E100–17, doi:<a href=\"https://doi.org/10.1086/734083\">10.1086/734083</a>.","ieee":"A. Nabeel <i>et al.</i>, “Discovering stochastic dynamical equations from ecological time series data,” <i>The American Naturalist</i>, vol. 205, no. 4. University of Chicago Press, pp. E100–E117, 2025.","apa":"Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Raj M, D., &#38; Guttal, V. (2025). Discovering stochastic dynamical equations from ecological time series data. <i>The American Naturalist</i>. University of Chicago Press. <a href=\"https://doi.org/10.1086/734083\">https://doi.org/10.1086/734083</a>","short":"A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, D. Raj M, V. Guttal, The American Naturalist 205 (2025) E100–E117.","ista":"Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Raj M D, Guttal V. 2025. Discovering stochastic dynamical equations from ecological time series data. The American Naturalist. 205(4), E100–E117."},"_id":"20056","page":"E100-E117","date_updated":"2025-09-30T14:14:43Z","isi":1,"arxiv":1,"title":"Discovering stochastic dynamical equations from ecological time series data","author":[{"full_name":"Nabeel, Arshed","last_name":"Nabeel","first_name":"Arshed"},{"full_name":"Karichannavar, Ashwin","last_name":"Karichannavar","first_name":"Ashwin"},{"full_name":"Palathingal, Shuaib","first_name":"Shuaib","last_name":"Palathingal"},{"full_name":"Jhawar, Jitesh","last_name":"Jhawar","first_name":"Jitesh"},{"full_name":"Brückner, David","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","orcid":"0000-0001-7205-2975"},{"last_name":"Raj M","first_name":"Danny","full_name":"Raj M, Danny"},{"full_name":"Guttal, Vishwesha","first_name":"Vishwesha","last_name":"Guttal"}],"date_published":"2025-04-01T00:00:00Z","type":"journal_article","publication":"The American Naturalist","article_processing_charge":"No","publication_identifier":{"eissn":["1537-5323"],"issn":["0003-0147"]},"quality_controlled":"1"},{"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2025-07-31T09:11:09Z","success":1,"file_name":"2025_Biology_Rosani.pdf","date_created":"2025-07-31T09:11:09Z","file_size":1885781,"checksum":"f5e059e66803fa54249c1db029aef0f6","file_id":"20097","creator":"dernst"}],"month":"07","_id":"20077","date_updated":"2025-09-30T14:10:07Z","citation":{"chicago":"Rosani, Umberto, Nehir Altan, Paola Venier, Enrico Bortoletto, Nicola Volpi, and Carrie Bernecky. “Ancestral Origin and Functional Expression of a Hyaluronic Acid Pathway Complement in Mussels.” <i>Biology</i>. MDPI, 2025. <a href=\"https://doi.org/10.3390/biology14080930\">https://doi.org/10.3390/biology14080930</a>.","ieee":"U. Rosani, N. Altan, P. Venier, E. Bortoletto, N. Volpi, and C. Bernecky, “Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels,” <i>Biology</i>, vol. 14, no. 8. MDPI, 2025.","ama":"Rosani U, Altan N, Venier P, Bortoletto E, Volpi N, Bernecky C. Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels. <i>Biology</i>. 2025;14(8). doi:<a href=\"https://doi.org/10.3390/biology14080930\">10.3390/biology14080930</a>","mla":"Rosani, Umberto, et al. “Ancestral Origin and Functional Expression of a Hyaluronic Acid Pathway Complement in Mussels.” <i>Biology</i>, vol. 14, no. 8, 930, MDPI, 2025, doi:<a href=\"https://doi.org/10.3390/biology14080930\">10.3390/biology14080930</a>.","ista":"Rosani U, Altan N, Venier P, Bortoletto E, Volpi N, Bernecky C. 2025. Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels. Biology. 14(8), 930.","apa":"Rosani, U., Altan, N., Venier, P., Bortoletto, E., Volpi, N., &#38; Bernecky, C. (2025). Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels. <i>Biology</i>. MDPI. <a href=\"https://doi.org/10.3390/biology14080930\">https://doi.org/10.3390/biology14080930</a>","short":"U. Rosani, N. Altan, P. Venier, E. Bortoletto, N. Volpi, C. Bernecky, Biology 14 (2025)."},"publisher":"MDPI","language":[{"iso":"eng"}],"year":"2025","acknowledgement":"This research was funded by the Italian Ministry of University and Research (MIUR), grant ID: P2022JEEMT (Developing a tool for the study of haplotype diversity in Mytilus galloprovincialis (HAMIGA)).","OA_place":"publisher","publication_identifier":{"issn":["2079-7737"]},"quality_controlled":"1","article_processing_charge":"Yes","ddc":["570"],"publication":"Biology","type":"journal_article","has_accepted_license":"1","date_published":"2025-07-24T00:00:00Z","DOAJ_listed":"1","title":"Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels","author":[{"first_name":"Umberto","last_name":"Rosani","full_name":"Rosani, Umberto"},{"full_name":"Altan, Nehir","last_name":"Altan","first_name":"Nehir"},{"last_name":"Venier","first_name":"Paola","full_name":"Venier, Paola"},{"first_name":"Enrico","last_name":"Bortoletto","full_name":"Bortoletto, Enrico"},{"last_name":"Volpi","first_name":"Nicola","full_name":"Volpi, Nicola"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","last_name":"Bernecky","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036"}],"isi":1,"day":"24","doi":"10.3390/biology14080930","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"CaBe"}],"status":"public","publication_status":"published","file_date_updated":"2025-07-31T09:11:09Z","oa":1,"issue":"8","PlanS_conform":"1","intvolume":"        14","external_id":{"isi":["001557922100001"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"930","abstract":[{"lang":"eng","text":"Hyaluronic acid (HA) is a key extracellular matrix component of vertebrates, where it mediates cell adhesion, immune regulation, and tissue remodeling through its interaction with specific receptors. Although HA has been detected in a few invertebrate species, the lack of fundamental components of the molecular HA pathway poses relevant objections about its functional role in these species. Mining genomic and transcriptomic data, we considered the conservation of the gene locus encoding for the extracellular link protein (XLINK) in marine mussels as well as its expression patterns. Structural and phylogenetic analyses were undertaken to evaluate possible similarities with vertebrate orthologs and to infer the origin of this gene in invertebrates. Biochemical analysis was used to quantify HA in tissues of Mytilus galloprovincialis. As a result, we confirm that the mussel can produce HA (up to 1.02 ng/mg in mantle) and that its genome encodes two XLINK gene loci. These loci are conserved in Mytilidae species and show a complex evolutionary path. Mussel XLINK genes appeared to be expressed during developmental stages in three mussel species, ranking in the top 100 expressed genes in M. trossulus at 17 h post-fertilization. In conclusion, the presence of HA and an active gene with the potential to bind HA suggests that mussels have the potential to synthesize and use HA and are among the few invertebrates encoding this gene."}],"date_created":"2025-07-25T08:28:26Z","volume":14,"article_type":"original","oa_version":"Published Version","OA_type":"gold"},{"publication":"Reproductive Biomedicine Online","article_processing_charge":"No","publication_identifier":{"eissn":["1472-6491"],"issn":["1472-6483"]},"quality_controlled":"1","isi":1,"title":"LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression","author":[{"first_name":"Iveta","last_name":"Yotova","full_name":"Yotova, Iveta"},{"full_name":"Proestling, Katharina","first_name":"Katharina","last_name":"Proestling"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048"},{"last_name":"Rainer","first_name":"Lisa","full_name":"Rainer, Lisa"},{"last_name":"Kaup","first_name":"Leonie","full_name":"Kaup, Leonie"},{"full_name":"Heine, Jana","last_name":"Heine","first_name":"Jana"},{"last_name":"Sandrieser","first_name":"Lejla","full_name":"Sandrieser, Lejla"},{"full_name":"Wenzl, René","first_name":"René","last_name":"Wenzl"},{"full_name":"Hudson, Quanah J.","last_name":"Hudson","first_name":"Quanah J."}],"date_published":"2025-07-17T00:00:00Z","type":"journal_article","publisher":"Elsevier","language":[{"iso":"eng"}],"month":"07","_id":"20079","citation":{"chicago":"Yotova, Iveta, Katharina Proestling, Florian Pauler, Lisa Rainer, Leonie Kaup, Jana Heine, Lejla Sandrieser, René Wenzl, and Quanah J. Hudson. “LINC01638 Promotes Epithelial-to-Mesenchymal Transition in Endometriosis Epithelial Cells by up-Regulating RHOB via HDAC1 Suppression.” <i>Reproductive Biomedicine Online</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">https://doi.org/10.1016/j.rbmo.2025.104942</a>.","mla":"Yotova, Iveta, et al. “LINC01638 Promotes Epithelial-to-Mesenchymal Transition in Endometriosis Epithelial Cells by up-Regulating RHOB via HDAC1 Suppression.” <i>Reproductive Biomedicine Online</i>, vol. 51, no. 3, 104942, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">10.1016/j.rbmo.2025.104942</a>.","ama":"Yotova I, Proestling K, Pauler F, et al. LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. <i>Reproductive Biomedicine Online</i>. 2025;51(3). doi:<a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">10.1016/j.rbmo.2025.104942</a>","ieee":"I. Yotova <i>et al.</i>, “LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression,” <i>Reproductive Biomedicine Online</i>, vol. 51, no. 3. Elsevier, 2025.","apa":"Yotova, I., Proestling, K., Pauler, F., Rainer, L., Kaup, L., Heine, J., … Hudson, Q. J. (2025). LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. <i>Reproductive Biomedicine Online</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">https://doi.org/10.1016/j.rbmo.2025.104942</a>","short":"I. Yotova, K. Proestling, F. Pauler, L. Rainer, L. Kaup, J. Heine, L. Sandrieser, R. Wenzl, Q.J. Hudson, Reproductive Biomedicine Online 51 (2025).","ista":"Yotova I, Proestling K, Pauler F, Rainer L, Kaup L, Heine J, Sandrieser L, Wenzl R, Hudson QJ. 2025. LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. Reproductive Biomedicine Online. 51(3), 104942."},"date_updated":"2025-09-30T14:10:46Z","acknowledgement":"The authors wish to thank all the participants and health professionals involved in this study. In addition, the authors wish to thank technical assistants Barbara Widmar, Matthias Witzmann-Stern and Isabella Haslinger for their work assisting with this study; and Simon Hippenmeyer for access to bioinformatic infrastructure and resources.\r\nOpen access funding was provided by the Medical University of Vienna.","year":"2025","scopus_import":"1","external_id":{"pmid":["40680553"],"isi":["001549819000002"]},"intvolume":"        51","OA_type":"closed access","pmid":1,"oa_version":"None","volume":51,"date_created":"2025-07-27T22:01:25Z","article_type":"original","article_number":"104942","abstract":[{"lang":"eng","text":"Research question: Is LINC01638 involved in regulation of epithelial-to-mesenchymal transition (EMT) in endometriosis?\r\nDesign: A prospective patient cohort study was combined with functional experiments in the 12Z endometriosis epithelial cell line to investigate the role of LINC01638 in endometriosis. Eutopic endometrial samples were collected by curettage, and ectopic endometrial lesion samples were collected by laparoscopic surgery from 24 control patients and 41 patients with endometriosis. The phenotype of 12Z cells was assessed following LINC01638 knockdown using siRNA, performing proliferation, adhesion, migration and invasion assays, as well as assessing apoptosis and cell cycle changes with flow cytometry assays. In order to assess the relationship between LINC01638 and histone deacetylase class 1 enzyme (HDAC1), LINC01638 knockdown was combined with HDAC inhibition with the specific HDAC inhibitor romidepsin.\r\nResults: LINC01638 was up-regulated in the epithelial layer of endometriotic lesions, and LINC01638 knockdown in 12Z cells led to reduced proliferation, adhesion, migration and invasion. The reduction in proliferation was associated with increased p21 and p27 expression, and G1 phase arrest. Further analysis of LINC01638 control and knockdown cells revealed that a number of transcription factors associated with EMT are down-regulated in knockdown cells, along with the cytoskeleton regulatory gene RHOB, while HDAC1 was up-regulated. Chromatin immunoprecipitation analysis and HDAC1 inhibitory treatment combined with LINC01638 knockdown indicated that LINC01638 regulates RHOB expression via HDAC1-mediated promoter deacetylation. RHOB is up-regulated in the epithelial layer of endometriotic lesions compared with eutopic endometrium, supporting a role in the disease.\r\nConclusions: LINC01638 is an epigenetic regulator of the pathogenesis of endometriosis, promoting proliferation and EMT of endometriotic lesions."}],"publication_status":"published","status":"public","doi":"10.1016/j.rbmo.2025.104942","department":[{"_id":"SiHi"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"17","issue":"3"},{"language":[{"iso":"eng"}],"publisher":"IEEE","date_updated":"2026-02-16T11:49:40Z","_id":"20081","citation":{"chicago":"Esposito, Amedeo Roberto, Michael Gastpar, and Ibrahim Issa. “Sibson α-Mutual Information and Its Variational Representations.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2025. <a href=\"https://doi.org/10.1109/TIT.2025.3587340\">https://doi.org/10.1109/TIT.2025.3587340</a>.","ama":"Esposito AR, Gastpar M, Issa I. Sibson α-mutual information and its variational representations. <i>IEEE Transactions on Information Theory</i>. 2025. doi:<a href=\"https://doi.org/10.1109/TIT.2025.3587340\">10.1109/TIT.2025.3587340</a>","mla":"Esposito, Amedeo Roberto, et al. “Sibson α-Mutual Information and Its Variational Representations.” <i>IEEE Transactions on Information Theory</i>, IEEE, 2025, doi:<a href=\"https://doi.org/10.1109/TIT.2025.3587340\">10.1109/TIT.2025.3587340</a>.","ieee":"A. R. Esposito, M. Gastpar, and I. Issa, “Sibson α-mutual information and its variational representations,” <i>IEEE Transactions on Information Theory</i>. IEEE, 2025.","short":"A.R. Esposito, M. Gastpar, I. Issa, IEEE Transactions on Information Theory (2025).","apa":"Esposito, A. R., Gastpar, M., &#38; Issa, I. (2025). Sibson α-mutual information and its variational representations. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2025.3587340\">https://doi.org/10.1109/TIT.2025.3587340</a>","ista":"Esposito AR, Gastpar M, Issa I. 2025. Sibson α-mutual information and its variational representations. IEEE Transactions on Information Theory."},"month":"07","OA_place":"repository","year":"2025","publication":"IEEE Transactions on Information Theory","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"arxiv":1,"author":[{"last_name":"Esposito","id":"9583e921-e1ad-11ec-9862-cef099626dc9","first_name":"Amedeo Roberto","full_name":"Esposito, Amedeo Roberto"},{"last_name":"Gastpar","first_name":"Michael","full_name":"Gastpar, Michael"},{"full_name":"Issa, Ibrahim","last_name":"Issa","first_name":"Ibrahim"}],"title":"Sibson α-mutual information and its variational representations","date_published":"2025-07-11T00:00:00Z","type":"journal_article","publication_status":"epub_ahead","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaMo"}],"doi":"10.1109/TIT.2025.3587340","day":"11","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.08352"}],"scopus_import":"1","external_id":{"arxiv":["2405.08352"]},"OA_type":"green","oa_version":"Preprint","article_type":"original","date_created":"2025-07-27T22:01:26Z","abstract":[{"lang":"eng","text":"Information measures can be constructed from Rényi divergences much like mutual information from Kullback-Leibler divergence. One such information measure is known as Sibson α-mutual information and has received renewed attention recently in several contexts: concentration of measure under dependence, statistical learning, hypothesis testing, and estimation theory. In this paper, we survey and extend the state of the art. In particular, we introduce variational representations for Sibson α-mutual information and employ them in each described context to derive novel results. Namely, we produce generalized Transportation-Cost inequalities and Fano-type inequalities. We also present an overview of known applications, spanning from learning theory and Bayesian risk to universal prediction."}]},{"ec_funded":1,"title":"Sustainable development key to limiting climate change-driven wildfire damages","author":[{"full_name":"Hwong, Yi-Ling","first_name":"Yi-Ling","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","last_name":"Hwong","orcid":"0000-0001-9281-3479"},{"first_name":"Edward","last_name":"Byers","full_name":"Byers, Edward"},{"first_name":"Michaela","last_name":"Werning","full_name":"Werning, Michaela"},{"last_name":"Quilcaille","first_name":"Yann","full_name":"Quilcaille, Yann"}],"date_published":"2025-07-15T00:00:00Z","DOAJ_listed":"1","type":"journal_article","has_accepted_license":"1","publication":"Environmental Research: Climate","ddc":["550"],"article_processing_charge":"Yes","publication_identifier":{"eissn":["2752-5295"]},"quality_controlled":"1","acknowledgement":"We thank Marina Andrijevic, Giacomo Falchetta, Samuel Lüthi, Caroline Muller, Carl Schleussner, and Adriano Vinca for providing useful ideas and feedback for this work. YLH is supported by funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska‐Curie Grant No. 101034413. EB, MW, and YQ are supported by the European Union’s Horizon Europe research and innovation programme under Grant Agreement No. 101081369 (SPARCCLE). We also thank the two anonymous reviewers for providing helpful feedback that greatly improved this manuscript.","OA_place":"publisher","year":"2025","publisher":"IOP Publishing","corr_author":"1","language":[{"iso":"eng"}],"month":"07","citation":{"ista":"Hwong Y-L, Byers E, Werning M, Quilcaille Y. 2025. Sustainable development key to limiting climate change-driven wildfire damages. Environmental Research: Climate. 4(3), 035005.","short":"Y.-L. Hwong, E. Byers, M. Werning, Y. Quilcaille, Environmental Research: Climate 4 (2025).","apa":"Hwong, Y.-L., Byers, E., Werning, M., &#38; Quilcaille, Y. (2025). Sustainable development key to limiting climate change-driven wildfire damages. <i>Environmental Research: Climate</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2752-5295/adec11\">https://doi.org/10.1088/2752-5295/adec11</a>","ieee":"Y.-L. Hwong, E. Byers, M. Werning, and Y. Quilcaille, “Sustainable development key to limiting climate change-driven wildfire damages,” <i>Environmental Research: Climate</i>, vol. 4, no. 3. IOP Publishing, 2025.","mla":"Hwong, Yi-Ling, et al. “Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.” <i>Environmental Research: Climate</i>, vol. 4, no. 3, 035005, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/2752-5295/adec11\">10.1088/2752-5295/adec11</a>.","ama":"Hwong Y-L, Byers E, Werning M, Quilcaille Y. Sustainable development key to limiting climate change-driven wildfire damages. <i>Environmental Research: Climate</i>. 2025;4(3). doi:<a href=\"https://doi.org/10.1088/2752-5295/adec11\">10.1088/2752-5295/adec11</a>","chicago":"Hwong, Yi-Ling, Edward Byers, Michaela Werning, and Yann Quilcaille. “Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.” <i>Environmental Research: Climate</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/2752-5295/adec11\">https://doi.org/10.1088/2752-5295/adec11</a>."},"_id":"20098","date_updated":"2025-08-04T07:46:33Z","file":[{"success":1,"access_level":"open_access","date_updated":"2025-08-04T07:38:14Z","relation":"main_file","content_type":"application/pdf","creator":"dernst","file_id":"20108","date_created":"2025-08-04T07:38:14Z","file_size":2807041,"checksum":"ca679496767021e792b0378c48fdee8c","file_name":"2025_EnvironResearchClimate_Hwong.pdf"}],"OA_type":"gold","oa_version":"Published Version","date_created":"2025-07-31T14:03:16Z","volume":4,"article_type":"original","related_material":{"record":[{"relation":"research_data","id":"20107","status":"public"}]},"article_number":"035005","abstract":[{"lang":"eng","text":"Climate change is causing wildfires to become more frequent and intense. While predicting burned areas using bioclimatic and anthropogenic factors is an active research area, few studies have examined what drives the economic damages of wildfires. Our study aims to fill this gap by analyzing key factors influencing global economic wildfire damages and projecting future damages under three shared socioeconomic pathways (SSPs). We apply regression analyses to identify significant predictors of economic wildfire damages at country levels and use the fitted model to project future damages under SSP126, SSP245, and SSP370. Results show that the human vulnerability index (HVI), reflecting socioeconomic conditions, is the strongest predictor of historical wildfire damages, followed by water vapor pressure deficit during the fire season and population density around forested areas. We found high population density to be associated with lower damages. These findings contrast with studies of burned areas, where climate factors are more dominant. Our model projects that by 2070, average global economic wildfire damages will be three times higher under SSP370 than SSP126. Our model also shows that following SSP126 not only reduces wildfire damages but also lessens the inequalities in damage distribution across countries. This pathway’s dual focus on equitable socioeconomic progress and climate action potentially enhances a country’s resilience that helps mitigate wildfire damages. Our analyses also indicate that strong socioeconomic development can offset wildfire damages associated with climate hazards, although this is less certain under SSP370. SSP126’s integrated approach improves both socioeconomic conditions and limits global warming, providing substantial benefits to less developed countries while still reducing damages in developed nations, despite their already low HVI scores. Our work complements existing research on burned areas and underscores the importance of sustainable development and international collaboration in reducing the economic damages of wildfires."}],"scopus_import":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"         4","PlanS_conform":"1","issue":"3","oa":1,"file_date_updated":"2025-08-04T07:38:14Z","publication_status":"published","status":"public","doi":"10.1088/2752-5295/adec11","department":[{"_id":"CaMu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"day":"15"},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"doi":"10.1016/j.celrep.2025.116080","department":[{"_id":"PeJo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020"},{"name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020","grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9"},{"grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"publication_status":"published","status":"public","file_date_updated":"2025-08-04T06:53:07Z","oa":1,"PlanS_conform":"1","issue":"8","intvolume":"        44","scopus_import":"1","external_id":{"isi":["001544472300002"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":44,"date_created":"2025-08-03T22:01:30Z","article_type":"original","article_number":"116080","abstract":[{"text":"The hippocampus, critical for learning and memory, is dogmatically described as a trisynaptic circuit where dentate gyrus granule cells (GCs), CA3 pyramidal neurons (PNs), and CA1 PNs are serially connected. However, CA3 also forms an autoassociative network, and its PNs have diverse morphologies, intrinsic properties, and GC input levels. How PN subtypes compose this recurrent network is unknown. To determine the synaptic arrangement of identified CA3 PNs, we combine multicellular patch-clamp recording and post hoc morphological analysis in mouse hippocampal slices. PNs can be divided into distinct “superficial” and “deep” subclasses, the latter including previously reported “athorny” cells. Subclasses have distinct input-output transformations and asymmetric connectivity, which is more abundant from superficial to deep PNs, splitting CA3 locally into two parallel recurrent networks. Coincident spontaneous inhibition occurs frequently within but not between subclasses, implying subclass-specific inhibitory innervation. Our results suggest two separately controlled sublayers for parallel information processing in hippocampal CA3.","lang":"eng"}],"OA_type":"gold","oa_version":"Published Version","file":[{"file_size":27695214,"checksum":"556ff9760661ecd23949d75031043b1f","date_created":"2025-08-04T06:53:07Z","file_name":"2025_CellReports_Watson.pdf","creator":"dernst","file_id":"20106","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2025-08-04T06:53:07Z"}],"corr_author":"1","publisher":"Elsevier","language":[{"iso":"eng"}],"month":"08","_id":"20099","date_updated":"2025-09-30T14:12:02Z","citation":{"chicago":"Watson, Jake, Victor M Vargas Barroso, and Peter M Jonas. “Cell-Specific Wiring Routes Information Flow through Hippocampal CA3.” <i>Cell Reports</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">https://doi.org/10.1016/j.celrep.2025.116080</a>.","ista":"Watson J, Vargas Barroso VM, Jonas PM. 2025. Cell-specific wiring routes information flow through hippocampal CA3. Cell Reports. 44(8), 116080.","short":"J. Watson, V.M. Vargas Barroso, P.M. Jonas, Cell Reports 44 (2025).","apa":"Watson, J., Vargas Barroso, V. M., &#38; Jonas, P. M. (2025). Cell-specific wiring routes information flow through hippocampal CA3. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">https://doi.org/10.1016/j.celrep.2025.116080</a>","ieee":"J. Watson, V. M. Vargas Barroso, and P. M. Jonas, “Cell-specific wiring routes information flow through hippocampal CA3,” <i>Cell Reports</i>, vol. 44, no. 8. Elsevier, 2025.","ama":"Watson J, Vargas Barroso VM, Jonas PM. Cell-specific wiring routes information flow through hippocampal CA3. <i>Cell Reports</i>. 2025;44(8). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">10.1016/j.celrep.2025.116080</a>","mla":"Watson, Jake, et al. “Cell-Specific Wiring Routes Information Flow through Hippocampal CA3.” <i>Cell Reports</i>, vol. 44, no. 8, 116080, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">10.1016/j.celrep.2025.116080</a>."},"year":"2025","acknowledgement":"We thank Andrea Navas-Olive and Rebecca J. Morse-Mora for critically reading an earlier version of the manuscript. We also thank Florian Marr and Christina Altmutter for excellent technical assistance, Alois Schlögl for programming and data-handling assistance, Todor Asenov for technical support, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA. We are particularly grateful for assistance from the Imaging and Optics Facility, Preclinical Facility, Lab Support Facility, and Miba Machine Shop. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692 to P.J., Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W., and an ISTplus Fellowship through Marie Skłodowska-Curie grant agreement no. 754411 to V.V.-B.), the Austrian Science Fund (P 36232-B, PAT 4178023, and Cluster of Excellence 10.55776/COE16 to P.J.), and a CONACyT fellowship (289638 to V.V.-B.) and was supported by a non-stipendiary EMBO fellowship (ALTF 756–2020 to J.F.W.).","OA_place":"publisher","article_processing_charge":"Yes","publication_identifier":{"eissn":["2211-1247"],"issn":["2639-1856"]},"quality_controlled":"1","publication":"Cell Reports","ddc":["570"],"date_published":"2025-08-01T00:00:00Z","DOAJ_listed":"1","type":"journal_article","has_accepted_license":"1","isi":1,"ec_funded":1,"title":"Cell-specific wiring routes information flow through hippocampal CA3","author":[{"orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","last_name":"Watson","full_name":"Watson, Jake"},{"first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","last_name":"Vargas Barroso","full_name":"Vargas Barroso, Victor M"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}]},{"PlanS_conform":"1","file_date_updated":"2025-08-04T06:25:23Z","oa":1,"status":"public","publication_status":"published","day":"27","department":[{"_id":"AlBr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.csbj.2025.07.039","oa_version":"Published Version","OA_type":"gold","abstract":[{"text":"A key step in protein structure prediction involves the detection of co-evolving pairs of residues, a signal for spatial proximity. This information is gleaned from multiple sequence alignment and underscores Alphafold’s structure prediction for almost every known protein. A simple means to create proteins beyond those found in nature, is by unnaturally fusing together two known proteins or protein parts. Here we demonstrate that structured peptides are predicted with significantly reduced accuracy when added to the terminal ends of scaffold proteins. Appending the multiple sequence alignment for the individual peptide tags to that of the scaffold protein often restores prediction accuracy. This work suggests that this windowed multiple sequence alignment approach can be a useful tool for predicting the structure of fused, chimeric proteins.","lang":"eng"}],"related_material":{"record":[{"status":"public","relation":"software","id":"20103"}],"link":[{"url":"https://github.com/sankethvedula/AFChimera","relation":"software"}]},"article_type":"original","volume":27,"date_created":"2025-08-03T22:01:31Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["001583543100001"]},"scopus_import":"1","intvolume":"        27","acknowledgement":"AM acknowledges the financial support of the Helmsley Fellowships Program for Sustainability and Health. AMB is supported by the Schmidt Chair in Artificial Intelligence.","OA_place":"publisher","year":"2025","citation":{"chicago":"Vedula, Sanketh, Alex M. Bronstein, and Ailie Marx. “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” <i>Computational and Structural Biotechnology Journal</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">https://doi.org/10.1016/j.csbj.2025.07.039</a>.","apa":"Vedula, S., Bronstein, A. M., &#38; Marx, A. (2025). Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment. <i>Computational and Structural Biotechnology Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">https://doi.org/10.1016/j.csbj.2025.07.039</a>","short":"S. Vedula, A.M. Bronstein, A. Marx, Computational and Structural Biotechnology Journal 27 (2025) 3292–3298.","ista":"Vedula S, Bronstein AM, Marx A. 2025. Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment. Computational and Structural Biotechnology Journal. 27, 3292–3298.","ama":"Vedula S, Bronstein AM, Marx A. Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment. <i>Computational and Structural Biotechnology Journal</i>. 2025;27:3292-3298. doi:<a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">10.1016/j.csbj.2025.07.039</a>","mla":"Vedula, Sanketh, et al. “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” <i>Computational and Structural Biotechnology Journal</i>, vol. 27, Elsevier, 2025, pp. 3292–98, doi:<a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">10.1016/j.csbj.2025.07.039</a>.","ieee":"S. Vedula, A. M. Bronstein, and A. Marx, “Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment,” <i>Computational and Structural Biotechnology Journal</i>, vol. 27. Elsevier, pp. 3292–3298, 2025."},"_id":"20100","page":"3292-3298","date_updated":"2025-11-27T14:09:59Z","month":"06","language":[{"iso":"eng"}],"publisher":"Elsevier","file":[{"file_name":"2025_CompStrucBiotechJour_Vedula.pdf","date_created":"2025-08-04T06:25:23Z","file_size":6609770,"checksum":"78d01f30fc1dc11dd2bd1d7bb7ac8a62","file_id":"20104","creator":"dernst","content_type":"application/pdf","relation":"main_file","date_updated":"2025-08-04T06:25:23Z","access_level":"open_access","success":1}],"author":[{"id":"94f2fe44-70fa-11f0-b76b-92922c09452b","first_name":"Sanketh","last_name":"Vedula","full_name":"Vedula, Sanketh"},{"orcid":"0000-0001-9699-8730","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander","last_name":"Bronstein","full_name":"Bronstein, Alexander"},{"full_name":"Marx, Ailie","last_name":"Marx","first_name":"Ailie"}],"title":"Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment","isi":1,"has_accepted_license":"1","type":"journal_article","DOAJ_listed":"1","date_published":"2025-06-27T00:00:00Z","ddc":["000","570"],"publication":"Computational and Structural Biotechnology Journal","quality_controlled":"1","publication_identifier":{"eissn":["2001-0370"]},"article_processing_charge":"Yes"},{"publication_status":"published","status":"public","doi":"10.1038/s41586-025-09241-2","department":[{"_id":"GradSch"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"23","oa":1,"file_date_updated":"2025-12-30T07:39:45Z","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"external_id":{"pmid":["40702175"]},"intvolume":"       645","OA_type":"hybrid","pmid":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","date_created":"2025-08-03T22:01:31Z","volume":645,"article_type":"original","related_material":{"record":[{"status":"public","id":"20883","relation":"research_data"}]},"abstract":[{"lang":"eng","text":"Evading imminent threat from predators is critical for animal survival. Effective defensive strategies can vary, even between closely related species. However, the neural basis of such species-specific behaviours remains poorly understood1,2,3,4. Here we find that two sister species of deer mice (genus Peromyscus)5 show different responses to the same looming stimulus: Peromyscus maniculatus, which occupies densely vegetated habitats, predominantly escapes, whereas the open field specialist, Peromyscus polionotus, briefly freezes. This difference arises from species-specific escape thresholds, is largely context-independent, and can be triggered by both visual and auditory threat stimuli. Using immunohistochemistry and electrophysiological recordings, we find that although visual threat activates the superior colliculus in both species, the role of the dorsal periaqueductal grey (dPAG) in driving behaviour differs. Whereas dPAG activity scales with running speed in P. maniculatus, neural activity in the dPAG of P. polionotus correlates poorly with movement, including during visually triggered escape. Moreover, optogenetic activation of dPAG neurons elicits acceleration in P. maniculatus but not in P. polionotus, and their chemogenetic inhibition during a looming stimulus delays escape onset in P. maniculatus to match that of P. polionotus. Together, we trace species-specific escape thresholds to a central circuit node, downstream of peripheral sensory neurons, localizing an ecologically relevant behavioural difference to a specific region of the mammalian brain."}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"month":"07","_id":"20101","date_updated":"2026-01-05T11:38:40Z","page":"439-447","citation":{"mla":"Baier, Felix, et al. “The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus Mice.” <i>Nature</i>, vol. 645, Springer Nature, 2025, pp. 439–47, doi:<a href=\"https://doi.org/10.1038/s41586-025-09241-2\">10.1038/s41586-025-09241-2</a>.","ama":"Baier F, Reinhard K, Nuttin B, et al. The neural basis of species-specific defensive behaviour in Peromyscus mice. <i>Nature</i>. 2025;645:439-447. doi:<a href=\"https://doi.org/10.1038/s41586-025-09241-2\">10.1038/s41586-025-09241-2</a>","ieee":"F. Baier <i>et al.</i>, “The neural basis of species-specific defensive behaviour in Peromyscus mice,” <i>Nature</i>, vol. 645. Springer Nature, pp. 439–447, 2025.","short":"F. Baier, K. Reinhard, B. Nuttin, A. Sans-Dublanc, C. Liu, V. Tong, J.S. Murmann, K. Wierda, K. Farrow, H.E. Hoekstra, Nature 645 (2025) 439–447.","apa":"Baier, F., Reinhard, K., Nuttin, B., Sans-Dublanc, A., Liu, C., Tong, V., … Hoekstra, H. E. (2025). The neural basis of species-specific defensive behaviour in Peromyscus mice. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-09241-2\">https://doi.org/10.1038/s41586-025-09241-2</a>","ista":"Baier F, Reinhard K, Nuttin B, Sans-Dublanc A, Liu C, Tong V, Murmann JS, Wierda K, Farrow K, Hoekstra HE. 2025. The neural basis of species-specific defensive behaviour in Peromyscus mice. Nature. 645, 439–447.","chicago":"Baier, Felix, Katja Reinhard, Bram Nuttin, Arnau Sans-Dublanc, Chen Liu, Victoria Tong, Julie Stefanie Murmann, Keimpe Wierda, Karl Farrow, and Hopi E. Hoekstra. “The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus Mice.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-09241-2\">https://doi.org/10.1038/s41586-025-09241-2</a>."},"file":[{"access_level":"open_access","date_updated":"2025-12-30T07:39:45Z","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"20884","creator":"dernst","file_name":"2025_Nature_Baier.pdf","date_created":"2025-12-30T07:39:45Z","checksum":"7ea846a7a49b3b2a248f6a27ab13d591","file_size":53301589}],"OA_place":"publisher","acknowledgement":"The authors thank M. Yilmaz, M. Meister, M. Joesch and T. Branco for advice on the behavioural experiments; C. Dulac, V. Bitsikas, E. Diel and J. Chen for advice on the immunohistochemistry and RNAscope experiments; J. Greenwood and E. Soucy for technical and engineering help; A. Chrzanowska for help and advice on optogenetic experiments; A. Calzoni for help aligning histological sections to a brain atlas; S. Worthington for statistical advice; P. Gonçalves for advice with the electrophysiology analysis; I. Vlaemick for help with whole cell experiments; R. Hellmiss for figure design; B. Sabatini, V. Stempel, K. Tyssowski and N. Sanguinetti for feedback on the manuscript; and Y. M. Lee and A. Tomcho for photos of P. maniculatus and P. leucopus habitats (Fig. 1). F.B. was supported by an HHMI International Student Research Fellowship, a Grant-in-Aid of the American Society of Mammalogy, a Herchel Smith Graduate Fellowship, a Robert A. Chapman Memorial Scholarship, and a Joan Brockman Williamson Fellowship. This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement 665501 and by the FWO (12S7917N and 12S7920N) to K.R. and from European Research Council (ERC) (grant agreement 101075848) to K.R. V.T. was supported by a Harvard PRISE fellowship and a Harvard Museum of Comparative Zoology grant for undergraduate research. K.F. is supported by the FWO (G094616N and G091719N) and the NIH (1R01EY032101). This work was supported by the Howard Hughes Medical Institute, of which H.E.H. was an Investigator.","year":"2025","publication":"Nature","ddc":["570"],"article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"quality_controlled":"1","title":"The neural basis of species-specific defensive behaviour in Peromyscus mice","author":[{"full_name":"Baier, Felix","last_name":"Baier","first_name":"Felix"},{"full_name":"Reinhard, Katja","first_name":"Katja","last_name":"Reinhard"},{"full_name":"Nuttin, Bram","last_name":"Nuttin","first_name":"Bram"},{"full_name":"Sans-Dublanc, Arnau","last_name":"Sans-Dublanc","first_name":"Arnau"},{"last_name":"Liu","first_name":"Chen","full_name":"Liu, Chen"},{"first_name":"Victoria","last_name":"Tong","full_name":"Tong, Victoria"},{"full_name":"Murmann, Julie Stefanie","id":"1d390868-f128-11eb-9611-a0ca5f7833b5","first_name":"Julie Stefanie","last_name":"Murmann"},{"full_name":"Wierda, Keimpe","last_name":"Wierda","first_name":"Keimpe"},{"last_name":"Farrow","first_name":"Karl","full_name":"Farrow, Karl"},{"first_name":"Hopi E.","last_name":"Hoekstra","full_name":"Hoekstra, Hopi E."}],"date_published":"2025-07-23T00:00:00Z","has_accepted_license":"1","type":"journal_article"},{"oa_version":"Published Version","OA_type":"hybrid","abstract":[{"lang":"eng","text":"Speciation is rarely observable directly. A way forward is to compare pairs of ecotypes that evolved in parallel in similar contexts but have reached different degrees of reproductive isolation. Such comparisons are possible in the marine snail Littorina saxatilis by contrasting barriers to gene flow between parallel ecotypes in Spain and Sweden. In both countries, divergent ecotypes have evolved to withstand either crab predation or wave action. Here, we explore transects spanning contact zones between the Crab and the Wave ecotypes using low-coverage whole-genome sequencing, morphological and behavioural traits. Despite parallel phenotypic divergence, distinct patterns of differentiation between the ecotypes emerged: a continuous cline in Sweden indicating a weak barrier to gene flow, but two highly genetically and phenotypically divergent, and partly spatially overlapping clusters in Spain suggesting a much stronger barrier to gene flow. The absence of Spanish early-generation hybrids supported strong isolation, but a low level of gene flow is evident from molecular data. In both countries, highly differentiated loci were located in both shared and country-specific chromosomal inversions but were also present in collinear regions. Despite being considered the same species and showing similar levels of phenotypic divergence, the Spanish ecotypes are much closer to full reproductive isolation than the Swedish ones. Barriers to gene flow of very different strengths between ecotypes within the same species might be explained by dissimilarities in the spatial arrangement of habitats, the selection gradients or the ages of the systems."}],"article_number":"e70025","article_type":"original","volume":34,"date_created":"2025-08-03T22:01:31Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["001538172800001"]},"scopus_import":"1","intvolume":"        34","issue":"21","PlanS_conform":"1","file_date_updated":"2025-12-30T09:25:17Z","oa":1,"status":"public","publication_status":"published","day":"01","department":[{"_id":"NiBa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1111/mec.70025","author":[{"full_name":"Raffini, Francesca","last_name":"Raffini","first_name":"Francesca"},{"first_name":"Aurélien","last_name":"De Jode","full_name":"De Jode, Aurélien"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Zagrodzka, Zuzanna B.","first_name":"Zuzanna B.","last_name":"Zagrodzka"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram"},{"full_name":"Galindo, Juan","first_name":"Juan","last_name":"Galindo"},{"full_name":"Rolán-Alvarez, Emilio","last_name":"Rolán-Alvarez","first_name":"Emilio"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"title":"Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail","isi":1,"type":"journal_article","has_accepted_license":"1","date_published":"2025-11-01T00:00:00Z","ddc":["570"],"publication":"Molecular Ecology","quality_controlled":"1","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"article_processing_charge":"Yes (in subscription journal)","OA_place":"publisher","acknowledgement":"This study was supported by European Research Council grant 693030-BARRIERS to RKB; the Swedish Research Council (grant number 2021-04191) to KJ; the Portuguese Foundation for Science and Technology (FCT: 2020.00275.CEECIND and PTDC/BIA-EVL/1614/2021) to RF; grant PID2022-137935NB-I00 by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU (ED431C 2020-05) to JG, grant PID2021-124930NB-I00 funded by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU to ERA, Xunta de Galicia (ED431C 2024/22), Centro singular de Investigación de Galicia accreditation 2024-2027 (ED431G 2023/07), ‘ERDF A way of making Europe’ and Norwegian Research Council RCN, project 315287 to AMW.","year":"2025","date_updated":"2025-12-30T09:25:45Z","_id":"20102","citation":{"chicago":"Raffini, Francesca, Aurélien De Jode, Kerstin Johannesson, Rui Faria, Zuzanna B. Zagrodzka, Anja M Westram, Juan Galindo, Emilio Rolán-Alvarez, and Roger K. Butlin. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes at Two Different Points on the Speciation Continuum in a Marine Snail.” <i>Molecular Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/mec.70025\">https://doi.org/10.1111/mec.70025</a>.","mla":"Raffini, Francesca, et al. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes at Two Different Points on the Speciation Continuum in a Marine Snail.” <i>Molecular Ecology</i>, vol. 34, no. 21, e70025, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70025\">10.1111/mec.70025</a>.","ama":"Raffini F, De Jode A, Johannesson K, et al. Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. <i>Molecular Ecology</i>. 2025;34(21). doi:<a href=\"https://doi.org/10.1111/mec.70025\">10.1111/mec.70025</a>","ieee":"F. Raffini <i>et al.</i>, “Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail,” <i>Molecular Ecology</i>, vol. 34, no. 21. Wiley, 2025.","apa":"Raffini, F., De Jode, A., Johannesson, K., Faria, R., Zagrodzka, Z. B., Westram, A. M., … Butlin, R. K. (2025). Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.70025\">https://doi.org/10.1111/mec.70025</a>","short":"F. Raffini, A. De Jode, K. Johannesson, R. Faria, Z.B. Zagrodzka, A.M. Westram, J. Galindo, E. Rolán-Alvarez, R.K. Butlin, Molecular Ecology 34 (2025).","ista":"Raffini F, De Jode A, Johannesson K, Faria R, Zagrodzka ZB, Westram AM, Galindo J, Rolán-Alvarez E, Butlin RK. 2025. Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. Molecular Ecology. 34(21), e70025."},"month":"11","language":[{"iso":"eng"}],"publisher":"Wiley","file":[{"file_id":"20906","creator":"dernst","file_name":"2025_MolecEcology_Raffini.pdf","date_created":"2025-12-30T09:25:17Z","checksum":"ec01edda64cfbc6cbc8adf300f719644","file_size":2767745,"date_updated":"2025-12-30T09:25:17Z","access_level":"open_access","success":1,"content_type":"application/pdf","relation":"main_file"}]}]